Dataset Information

HiPub: translating PubMed and PMC texts to networks for knowledge discovery.

ABSTRACT:

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We introduce HiPub, a seamless Chrome browser plug-in that automatically recognizes, annotates and translates biomedical entities from texts into networks for knowledge discovery. Using a combination of two different named-entity recognition resources, HiPub can recognize genes, proteins, diseases, drugs, mutations and cell lines in texts, and achieve high precision and recall. HiPub extracts biomedical entity-relationships from texts to construct context-specific networks, and integrates existing network data from external databases for knowledge discovery. It allows users to add additional entities from related articles, as well as user-defined entities for discovering new and unexpected entity-relationships. HiPub provides functional enrichment analysis on the biomedical entity network, and link-outs to external resources to assist users in learning new entities and relations.

Availability and implementation

HiPub and detailed user guide are available at http://hipub.korea.ac.kr

Contact

kangj@korea.ac.kr, aikchoon.tan@ucdenver.edu

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Lee K

PROVIDER: S-EPMC5018380 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature

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Publications

HiPub: translating PubMed and PMC texts to networks for knowledge discovery.

Lee Kyubum K Shin Wonho W Kim Byounggun B Lee Sunwon S Choi Yonghwa Y Kim Sunkyu S Jeon Minji M Tan Aik Choon AC Kang Jaewoo J

Bioinformatics (Oxford, England) 20160802 18

<h4>Unlabelled</h4>We introduce HiPub, a seamless Chrome browser plug-in that automatically recognizes, annotates and translates biomedical entities from texts into networks for knowledge discovery. Using a combination of two different named-entity recognition resources, HiPub can recognize genes, proteins, diseases, drugs, mutations and cell lines in texts, and achieve high precision and recall. HiPub extracts biomedical entity-relationships from texts to construct context-specific networks, an ...[more]

PMID: 27485446

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Project description:Open biomedical repositories, such as PubMed Central (PMC), are a means to make research discoverable and permanently accessible. Assessing the potential interest of key stakeholders in an Australasia PubMed Central was the objective of this research. The investigation is novel, assisting in the development of open science infrastructure through its systematic analysis of the potential interest in, and viability of a biomedical repository for managing openly accessible research outputs for the Australasia region. The research adopted a qualitative approach based on semi-structured interviews and a focus group. Forty-four stakeholders located throughout Australia and New Zealand participated in the research. Participants expanded upon their experience of PubMed, MEDLINE, PMC and their use of information resources for research and clinical practice. The Evidence Based Healthcare (EBHC) pyramid was the theoretical model adopted to explain open biomedical repository processes. A strengths, weaknesses, opportunities and threats (SWOT) analysis identified support for exploring membership of an international PMC system, in particular Europe PMC. Lessons learnt from PMC US, Europe PMC and PMC Canada (collectively known as PubMed Central International) informed the investigation. A major strength identified was that PubMed Central International has been able to achieve high levels of compliance way beyond that of most institutional repositories. A great threat faced is overcoming the difficulties of working together with other major world bodies and financially sustaining an Australasia PMC. Improving Australasian biomedical knowledge management processes may be possible from adopting a PMC for retrieving and transferring research, linked to the data underlying the research. This in turn could help put regional research under a brighter spotlight, potentially leading to improvements in research quality. There is an opportunity for a potential Australasia PMC to harvest biomedical research from the National Library of Australia's aggregator database, Trove and work closely with Europe PMC to avoid duplication of effort. Overall, establishment of an Australasia permanent biomedical digital open repository is perceived as important, with significant potential flow-on benefits to healthcare, industry and society.

Project description:BackgroundClinicians are faced with using the current best evidence to make treatment decisions, yet synthesis of knowledge translation (KT) strategies that influence professional practice behaviors in rehabilitation disciplines remains largely unknown.PurposeThe purposes of this study were: (1) to examine the state of science for KT strategies used in the rehabilitation professions (physical therapy, occupational therapy, speech-language pathology), (2) to identify the methodological approaches utilized in studies exploring KT strategies, and (3) to report the extent that KT interventions are described.Data sourcesEight electronic databases (MEDLINE, CINAHL, ERIC, PASCAL, EMBASE, IPA, Scopus, and CENTRAL) were searched from January 1985 to May 2013 using language (English) restriction.Study selectionEligibility criteria specified articles evaluating interventions or strategies with a primary purpose of translating research or enhancing research uptake into clinical practice.Data extractionTwo reviewers independently screened the titles and abstracts, reviewed full-text articles, performed data extraction, and performed quality assessment. The published descriptions of the KT interventions were compared with the Workgroup for Intervention Development and Evaluation Research's (WIDER) Recommendations to Improve the Reporting of the Content of Behaviour Change Interventions.Data synthesisOf a total of 2,793 articles located and titles and abstracts screened, 26 studies were included in the systematic review. Eighteen articles reported interventions that used a multicomponent KT strategy. Education-related components were the predominant KT intervention regardless of whether it was a single or multicomponent intervention. Few studies used reminders or audit and feedback intervention (n=3). Only one study's primary outcome measure was an economic evaluation. No clear delineation of the effect on KT strategies was seen.LimitationsDiverse studies were included; however, the heterogeneity of the studies was not conducive to pooling the data.ConclusionsThe modest-to-low methodological quality assessed in the studies underscores the gaps in KT strategies used in rehabilitation and highlights the need for rigorously designed studies that are well reported.

Dataset Information

HiPub: translating PubMed and PMC texts to networks for knowledge discovery.

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Availability and implementation

Contact

Supplementary information

Publications

HiPub: translating PubMed and PMC texts to networks for knowledge discovery.

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